Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_HGR-N1-BDNA-1_A23KFG7LT4_1/1029_HGR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/b5ea34978b24a23d2b5bcb62c9f40a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/b5ea34978b24a23d2b5bcb62c9f40a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_HGR-N1-BDNA-1_A23KFG7LT4_1/1029_HGR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_HGR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HGR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HGR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HGR-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 104627997 total, 63757 skipped (flags/unmapped)
Fragments: 52375072 total (52158300 tlen-paired, 3949 hash-paired, 494 singletons, 9581 discordant, 202748 orphans, 8669 too large [>5000 bp], 18528937 duplicates)
Reads: 114277957 total, 55501 skipped (flags/unmapped)
Fragments: 57215614 total (56974524 tlen-paired, 4238 hash-paired, 624 singletons, 7958 discordant, 228270 orphans, 10061 too large [>5000 bp], 19770381 duplicates)
Reads: 111447158 total, 57995 skipped (flags/unmapped)
Fragments: 55798609 total (55520976 tlen-paired, 4770 hash-paired, 462 singletons, 8904 discordant, 263497 orphans, 27952 too large [>5000 bp], 19687986 duplicates)
Reads: 122453532 total, 96529 skipped (flags/unmapped)
Fragments: 61378032 total (60759437 tlen-paired, 4361 hash-paired, 519 singletons, 120181 discordant, 493534 orphans, 47496 too large [>5000 bp], 21734930 duplicates)